Assessing Adaptation Of A Lentil (Lens culinaris Medik.) Diversity Panel To Temperature And Photoperiod

Introduction
R Code Vignette
Shiny App
Figures
- Figure 1
- Figure 2
- Figure 3
- Figure 4
- Figure 5
- Figure 6
- Figure 7
Supplemental Figures
Supplemental Tables
Animations
Additional Figures

Derek Wright, Sandesh Neupane, Taryn Heidecker, Teketel Haile, Clarice Coyne, Sripada Udupa, Eleonora Barilli, Diego Rubiales, Tania Gioia, Reena Mehra, Ashutosh Sarker, Rajeev Dhakal, Babul Anwar, Debashish Sarker, Albert Vandenberg, and Kirstin E. Bett

Introduction

Project Collaborators:

Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
United States Department of Agriculture Western Region Plant Introduction Station, Pullman, Washington, USA
International Center for Agriculture Research in the Dry Areas, Rabat, Morocco
Institute for Sustainable Agriculture, Spanish National Research Council, Cordoba, Spain
School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
International Center for Agriculture Research in the Dry Areas, New Delhi, India
Local Initiatives for Biodiversity, Research and Development, Pokhara, Nepal
Bangladesh Agricultural Research Institute, Jessore, Bangladesh

Project Sponsors:

Saskatchewan Pulse Growers Association
Western Grains Research Foundation
GenomePrairie
GenomeCanada
Saskatchewan Ministry of Agriculture

R Code Vignette

Phenology_Vignette.html

Phenology_Vignette.pdf

Shiny App

Download this folder and run app.R in R

Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Supplemental Figures

Supplemental Figure 1

Supplemental Figure 2

Supplemental Figure 3

Supplemental Figure 4

Supplemental Figure 5

Supplemental Figure 6

Supplemental Figure 7

Supplemental Figure 8

Supplemental Figure 9

Supplemental Figure 10

Supplemental Figure 11

Supplemental Tables

Supplemental Table 1

xx <- read.csv("Supplemental_Table_01.csv")
knitr::kable(xx[c(1:5,31:35,101:105,320:324),])

	Entry	Name	Origin	Source	Synonyms
1	1	CDC Asterix AGL	Canada	USASK
2	2	CDC Rosie AGL	Canada	USASK
3	3	3156-11 AGL	Canada	USASK
4	4	CDC Greenstar AGL	Canada	USASK
5	5	CDC Cherie AGL	Canada	USASK
31	31	CN 105777 AGL	Egypt	PGRC	LENS 170;B 47
32	32	CN 105789 AGL	Ethiopia	PGRC	LENS 184;B 136
33	33	CN 105791 AGL	Egypt	PGRC	LENS 190;B 32
34	34	CN 105862 AGL	Tunisia	PGRC	LENS 559
35	35	CN 105863 AGL	Tunisia	PGRC	LENS 561
101	101	ILL 6821 AGL	Ethiopia	ICARDA	IG 73685;FLIP 89-63L;ALEMAYA
102	102	ILL 6853 AGL	Syria	ICARDA	IG 73717
103	103	ILL 7089 AGL	Russia	ICARDA	IG 73953
104	104	ILL 7558 AGL	India	ICARDA	IG 76277
105	105	ILL 7663 AGL	ICARDA	ICARDA	IG 114665;FLIP 95-7L
320	320	W6 27754 LSP AGL	USDA	USDA
321	321	W6 27760 LSP AGL	USDA	USDA
322	322	W6 27763 LSP AGL	USDA	USDA
323	323	W6 27766 LSP AGL	USDA	USDA
324	324	W6 27767 LSP AGL	USDA	USDA

Supplemental Table 2

xx <- read.csv("Supplemental_Table_02.csv")
knitr::kable(xx)

Location	Year	Short.Name	Latitude	Longitude	Planting.Date	Temperature..mean.	Photoperiod..mean.	Number.of.Seeds.Sown	Plot.Type
Sutherland, Canada	2016	Su16	52.16770	-106.5054	2016-04-27	16.7	15.9	60	three, 1 meter rows
Rosthern, Canada	2016	Ro16	52.68920	-106.2945	2016-05-06	17.2	16.2	60	three, 1 meter rows
Marchouch, Morocco	2016	Mo16	33.62000	-6.7200	2016-11-21	12.0	10.8	25	one, 1 meter row
Cordoba, Spain	2016	Sp16	37.90000	-4.8000	2016-12-13	12.5	10.9	25	one, 1 meter row
Metaponto, Italy	2016	It16	40.39000	16.7800	2016-11-29	10.6	10.8	25	one, 1 meter row
Bhopal, India	2016	In16	23.11000	76.8800	2016-12-04	17.6	10.9	25	one, 1 meter row
Bardiya, Nepal	2016	Ne16	28.25000	81.5000	2016-11-14	19.2	11.0	25	one, 1 meter row
Jessore, Bangladesh	2016	Ba16	23.19000	89.1900	2016-11-15	18.6	10.8	25	one, 1 meter row
Sutherland, Canada	2017	Su17	52.16832	-106.5108	2017-05-04	15.7	16.1	70	three, 1 meter rows
Rosthern, Canada	2017	Ro17	52.69150	-106.2897	2017-05-19	17.5	16.4	70	three, 1 meter rows
Marchouch, Morocco	2017	Mo17	33.62000	-6.7200	2017-12-21	11.8	11.5	50	two, 1 meter rows
Cordoba, Spain	2017	Sp17	37.90000	-4.8000	2017-12-14	11.7	11.1	50	two, 1 meter rows
Metaponto, Italy	2017	It17	40.39000	16.7800	2017-11-28	11.2	10.8	50	two, 1 meter rows
Bhopal, India	2017	In17	23.11500	76.8850	2017-11-09	20.6	10.7	50	two, 1 meter rows
Jessore, Bangladesh	2017	Ba17	23.19500	89.1950	2017-12-03	21.7	11.0	50	two, 1 meter rows
Central Ferry, USA	2018	Us18	46.65000	-117.7600	2018-03-29	15.8	14.3	50	two, 1 meter rows
Sutherland, Canada	2018	Su18	52.16890	-106.5149	2018-05-09	17.6	16.1	70	three, 1 meter rows
Bardiya, Nepal	2017	Ne17	28.42000	81.8600	2017-11-03	19.4	10.8	50	two, 1 meter rows

Supplemental Table 3

xx <- read.csv("Supplemental_Table_03.csv")
knitr::kable(xx[c(1:2,61:62,201:202,647:648),])

	Entry	Name	a	b	c	d	RR	Environments	a_p.value	b_p.value	c_p.value	d_p.value
1	1	CDC Asterix AGL	-0.0187717	0.0003372	0.0020456	NA	0.8978347	16	0.0000000	0.0000001	0.0000000	NA
2	1	CDC Asterix AGL	0.0072693	-0.0012017	-0.0003174	0.0001397	0.8992827	16	0.6202032	0.1688352	0.8110850	0.0793975
61	31	CN 105777 AGL	-0.0203402	0.0006260	0.0020791	NA	0.8417776	18	0.0000000	0.0000000	0.0000000	NA
62	31	CN 105777 AGL	-0.0299805	0.0011958	0.0029539	-0.0000518	0.8473458	18	0.1417083	0.3178702	0.1107758	0.6321050
201	101	ILL 6821 AGL	-0.0207765	0.0001801	0.0024844	NA	0.9055885	14	0.0000000	0.0006591	0.0000000	NA
202	101	ILL 6821 AGL	-0.0149886	-0.0001621	0.0019592	0.0000311	0.9051060	14	0.2937562	0.8467141	0.1321410	0.6828037
647	324	W6 27767 LSP AGL	-0.0194010	0.0002353	0.0022805	NA	0.8697454	15	0.0000000	0.0000289	0.0000000	NA
648	324	W6 27767 LSP AGL	-0.0080395	-0.0004354	0.0012494	0.0000609	0.8679062	15	0.5871621	0.6178443	0.3531932	0.4421900

Supplemental Table 4

xx <- read.csv("Supplemental_Table_04.csv")
knitr::kable(rbind(head(xx), tail(xx)))

	Temperate_Location	SouthAsian_Location	Mediterranean_Location	RR	Genotypes
1	Ro17	In16	Sp16	0.461770	159
2	Su18	In16	Sp16	0.462242	159
3	Ro16	In16	Sp16	0.466809	159
4	Su17	In16	Sp16	0.469932	159
5	Su16	In16	Sp16	0.473691	159
6	Ro17	In16	It17	0.475920	159
211	Ro17	Ba17	Sp17	0.858843	291
212	Su16	Ba17	Mo16	0.858923	291
213	Ro16	Ba17	Sp17	0.859936	291
214	Us18	Ba17	Sp17	0.861168	289
215	Su17	Ba17	Sp17	0.862977	291
216	Su16	Ba17	Sp17	0.863054	291

Assessing Adaptation Of A Lentil (Lens culinaris Medik.) Diversity Panel To Temperature And Photoperiod

Assessing Adaptation Of A Lentil (Lens culinaris Medik.) Diversity Panel To Temperature And Photoperiod

Introduction

R Code Vignette

Shiny App

Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Supplemental Figures

Supplemental Figure 1

Supplemental Figure 2

Supplemental Figure 3

Supplemental Figure 4

Supplemental Figure 5

Supplemental Figure 6

Supplemental Figure 7

Supplemental Figure 8

Supplemental Figure 9

Supplemental Figure 10

Supplemental Figure 11

Supplemental Tables

Supplemental Table 1

Supplemental Table 2

Supplemental Table 3

Supplemental Table 4

Animations

Temperature and Photoperiod Regressions

Model Predictions

Photothermal Planes

Additional Figures

Additional Figure 1

Additional Figure 2

Additional Figure 3

Additional Figure 4

Additional Figure 5

Additional Figure 6

Additional Figure 7

Additional Figure 8

Additional Figure 9

Additional Figure 10

Additional Figure 11

Additional Figure 12

Additional Figure 13

Additional Figure 14